MicrobesOnline: an integrated portal for comparative and functional genomics

By Paramvir S. Dehal, marcin p. joachimiak, Morgan N. Price, John T. Bates, Jason K. Baumohl, Dylan Chivian, Gregory D. Friedland, Katherine H. Huang, Keith Keller, P. Novichkov and 3 more. Nucleic Acids Res., 2009

461 citations recorded by the source corpus.

Since 2003, MicrobesOnline (http://www.microbesonline.org) has been providing a community resource for comparative and functional genome analysis. The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. To assist in annotating genes and in reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources. The next update of MicrobesOnline will contain significant new functionality, including comparative analysis of metagenomic sequence data. Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/db26474775c7761841a04a24ebac60035220f990

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Citations in the corpus

RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria (2013, methodology): “Annotations of TF protein domains were collected from the MicrobesOnline database [39].”
BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata (2011, background): “Several other resources are collecting and presenting bio-molecular projects but all of them are limited in scope either by speciﬁc organism group [MicrobesOnline (9), IMG (10), GDR (11)] or by project type [GOLD (12)].”
FungiDB: an integrated functional genomics database for fungi (2011, background): “gov/fungi) and IMG tools (7) or Microbes Online (8), which provide complementary data query or visualization tools but do not have the data mining capabilities and broad cross-species comparisons that are possible with the WDK search interface.”
EDGAR 2.0: an enhanced software platform for comparative gene content analyses (2016, unknown): “Several software platforms for comparative gene content analyses have been developed in the last decade like IMG (3), MicrobesOnline (4), MBGD (5) or OrtholugeDB (6).”